Hi!
I’m not able to run nextstrain on my computer yet, but I’d like to know the data format behind the entropy panel. Would some augur subcommand generate a mutation file? If so, what kind of data is in there? Do you have an example?
I noticed on the tree, the external nodes have 0 or few mutations labeled. Are the mutations shown here only include those that are new when compared with the immediate parent?
Hi @yzhang2168 – the data in the entropy panel is generated within auspice (the visualisation app which is displaying the tree, entropy panel etc) from the mutations which have been inferred across the tree by augur. The augur commands which generate these are augur ancestral (infers nucleotide mutations up the tree) and augur translate (nt → aa). This section of the docs explains a bit more on what entropy & events mean, as well as showing how to download these data in TSV format from auspice. Note also that we mask certain sites in the genome for our SARS-CoV-2 analysis – details in the repo.
Are the mutations shown [on a branch/tip] only include those that are new when compared with the immediate parent?
Yes, that’s correct. If you change the tree view to “divergence” (via the controls in the sidebar) then you can see a count of nucleotide changes relative to the (inferred) root sequence.
P.S. If there’s a technical reason you haven’t been able to run nextstrain on your computer please let us know and we’ll try to help!